├── .gitattributes ├── .gitignore ├── .travis.yml ├── LICENSE ├── NOTICE ├── README.md ├── docs ├── .gitignore ├── YesWorkflowDB.pdf └── YesWorkflowDB.vpp ├── examples ├── .gitignore ├── Makefile ├── clean_name_date │ ├── clean_name_date_yw.py │ ├── date_val_log.txt │ ├── demo_input.csv │ ├── demo_localDB.csv │ ├── demo_output_name_date_val.csv │ ├── demo_output_name_val.csv │ ├── name_val_log.txt │ ├── record_id.txt │ └── yw │ │ ├── combined.pdf │ │ ├── combined.png │ │ ├── csv │ │ ├── extractfacts_annotation.csv │ │ ├── extractfacts_annotation_qualifies.csv │ │ ├── extractfacts_extract_source.csv │ │ ├── modelfacts_channel.csv │ │ ├── modelfacts_data.csv │ │ ├── modelfacts_function.csv │ │ ├── modelfacts_has_in_port.csv │ │ ├── modelfacts_has_out_port.csv │ │ ├── modelfacts_has_subprogram.csv │ │ ├── modelfacts_inflow_connects_to_channel.csv │ │ ├── modelfacts_log_template.csv │ │ ├── modelfacts_log_template_variable.csv │ │ ├── modelfacts_outflow_connects_to_channel.csv │ │ ├── modelfacts_port.csv │ │ ├── modelfacts_port_alias.csv │ │ ├── modelfacts_port_connects_to_channel.csv │ │ ├── modelfacts_port_uri_template.csv │ │ ├── modelfacts_program.csv │ │ ├── modelfacts_uri_variable.csv │ │ └── modelfacts_workflow.csv │ │ ├── dlv │ │ ├── extractfacts.dlv │ │ └── modelfacts.dlv │ │ ├── listing.txt │ │ ├── subgraph_date_val.pdf │ │ ├── subgraph_date_val.png │ │ ├── subgraph_name_val.pdf │ │ ├── subgraph_name_val.png │ │ ├── yw.properties │ │ ├── yw.properties.csv │ │ └── yw.properties.dlv ├── default_script_settings.sh └── simulate_data_collection │ ├── .yw_setup │ ├── Makefile │ ├── calibration.img │ ├── cassette_q55_spreadsheet.csv │ ├── extract_queries.sh │ ├── facts │ ├── yw_extract_facts.P │ ├── yw_model_facts.P │ ├── yw_recon_facts.P │ └── yw_views.P │ ├── graphs │ ├── yw_combined_graph.gv │ ├── yw_data_graph.gv │ ├── yw_process_graph.gv │ └── yw_prospective_lineage.gv │ ├── other_queries.sh │ ├── query.sh │ ├── query_outputs.txt │ ├── run │ ├── collected_images.csv │ ├── data │ │ ├── DRT240 │ │ │ ├── DRT240_10000eV_001.img │ │ │ ├── DRT240_10000eV_002.img │ │ │ ├── DRT240_10000eV_003.img │ │ │ ├── DRT240_10000eV_004.img │ │ │ ├── DRT240_10000eV_005.img │ │ │ ├── DRT240_10000eV_006.img │ │ │ ├── DRT240_10000eV_007.img │ │ │ ├── DRT240_10000eV_008.img │ │ │ ├── DRT240_10000eV_009.img │ │ │ ├── DRT240_10000eV_010.img │ │ │ ├── DRT240_10000eV_011.img │ │ │ ├── DRT240_10000eV_012.img │ │ │ ├── DRT240_10000eV_013.img │ │ │ ├── DRT240_10000eV_014.img │ │ │ ├── DRT240_10000eV_015.img │ │ │ ├── DRT240_10000eV_016.img │ │ │ ├── DRT240_10000eV_017.img │ │ │ ├── DRT240_10000eV_018.img │ │ │ ├── DRT240_10000eV_019.img │ │ │ ├── DRT240_10000eV_020.img │ │ │ ├── DRT240_10000eV_021.img │ │ │ ├── DRT240_10000eV_022.img │ │ │ ├── DRT240_10000eV_023.img │ │ │ ├── DRT240_10000eV_024.img │ │ │ ├── DRT240_10000eV_025.img │ │ │ ├── DRT240_10000eV_026.img │ │ │ ├── DRT240_10000eV_027.img │ │ │ ├── DRT240_10000eV_028.img │ │ │ ├── DRT240_10000eV_029.img │ │ │ ├── DRT240_10000eV_030.img │ │ │ ├── DRT240_10000eV_031.img │ │ │ ├── DRT240_10000eV_032.img │ │ │ ├── DRT240_10000eV_033.img │ │ │ ├── DRT240_10000eV_034.img │ │ │ ├── DRT240_10000eV_035.img │ │ │ ├── DRT240_10000eV_036.img │ │ │ ├── DRT240_10000eV_037.img │ │ │ ├── DRT240_10000eV_038.img │ │ │ ├── DRT240_10000eV_039.img │ │ │ ├── DRT240_10000eV_040.img │ │ │ ├── DRT240_10000eV_041.img │ │ │ ├── DRT240_10000eV_042.img │ │ │ ├── DRT240_10000eV_043.img │ │ │ ├── DRT240_10000eV_044.img │ │ │ ├── DRT240_10000eV_045.img │ │ │ ├── DRT240_10000eV_046.img │ │ │ ├── DRT240_10000eV_047.img │ │ │ ├── DRT240_11000eV_001.img │ │ │ ├── DRT240_11000eV_002.img │ │ │ ├── DRT240_11000eV_003.img │ │ │ ├── DRT240_11000eV_004.img │ │ │ ├── DRT240_11000eV_005.img │ │ │ ├── DRT240_11000eV_006.img │ │ │ ├── DRT240_11000eV_007.img │ │ │ ├── DRT240_11000eV_008.img │ │ │ ├── DRT240_11000eV_009.img │ │ │ ├── DRT240_11000eV_010.img │ │ │ ├── DRT240_11000eV_011.img │ │ │ ├── DRT240_11000eV_012.img │ │ │ ├── DRT240_11000eV_013.img │ │ │ ├── DRT240_11000eV_014.img │ │ │ ├── DRT240_11000eV_015.img │ │ │ ├── DRT240_11000eV_016.img │ │ │ ├── DRT240_11000eV_017.img │ │ │ ├── DRT240_11000eV_018.img │ │ │ ├── DRT240_11000eV_019.img │ │ │ ├── DRT240_11000eV_020.img │ │ │ ├── DRT240_11000eV_021.img │ │ │ ├── DRT240_11000eV_022.img │ │ │ ├── DRT240_11000eV_023.img │ │ │ ├── DRT240_11000eV_024.img │ │ │ ├── DRT240_11000eV_025.img │ │ │ ├── DRT240_11000eV_026.img │ │ │ ├── DRT240_11000eV_027.img │ │ │ ├── DRT240_11000eV_028.img │ │ │ ├── DRT240_11000eV_029.img │ │ │ ├── DRT240_11000eV_030.img │ │ │ ├── DRT240_11000eV_031.img │ │ │ ├── DRT240_11000eV_032.img │ │ │ ├── DRT240_11000eV_033.img │ │ │ ├── DRT240_11000eV_034.img │ │ │ ├── DRT240_11000eV_035.img │ │ │ ├── DRT240_11000eV_036.img │ │ │ ├── DRT240_11000eV_037.img │ │ │ ├── DRT240_11000eV_038.img │ │ │ ├── DRT240_11000eV_039.img │ │ │ ├── DRT240_11000eV_040.img │ │ │ ├── DRT240_11000eV_041.img │ │ │ ├── DRT240_11000eV_042.img │ │ │ ├── DRT240_11000eV_043.img │ │ │ ├── DRT240_11000eV_044.img │ │ │ ├── DRT240_11000eV_045.img │ │ │ ├── DRT240_11000eV_046.img │ │ │ ├── DRT240_11000eV_047.img │ │ │ ├── DRT240_12000eV_001.img │ │ │ ├── DRT240_12000eV_003.img │ │ │ ├── DRT240_12000eV_004.img │ │ │ ├── DRT240_12000eV_005.img │ │ │ ├── DRT240_12000eV_006.img │ │ │ ├── DRT240_12000eV_007.img │ │ │ ├── DRT240_12000eV_008.img │ │ │ ├── DRT240_12000eV_009.img │ │ │ ├── DRT240_12000eV_010.img │ │ │ ├── DRT240_12000eV_011.img │ │ │ ├── DRT240_12000eV_012.img │ │ │ ├── DRT240_12000eV_013.img │ │ │ ├── DRT240_12000eV_014.img │ │ │ ├── DRT240_12000eV_015.img │ │ │ ├── DRT240_12000eV_016.img │ │ │ ├── DRT240_12000eV_017.img │ │ │ ├── DRT240_12000eV_018.img │ │ │ ├── DRT240_12000eV_019.img │ │ │ ├── DRT240_12000eV_020.img │ │ │ ├── DRT240_12000eV_021.img │ │ │ ├── DRT240_12000eV_022.img │ │ │ ├── DRT240_12000eV_023.img │ │ │ ├── DRT240_12000eV_024.img │ │ │ ├── DRT240_12000eV_025.img │ │ │ ├── DRT240_12000eV_026.img │ │ │ ├── DRT240_12000eV_027.img │ │ │ ├── DRT240_12000eV_028.img │ │ │ ├── DRT240_12000eV_029.img │ │ │ ├── DRT240_12000eV_030.img │ │ │ ├── DRT240_12000eV_031.img │ │ │ ├── DRT240_12000eV_032.img │ │ │ ├── DRT240_12000eV_033.img │ │ │ ├── DRT240_12000eV_034.img │ │ │ ├── DRT240_12000eV_035.img │ │ │ ├── DRT240_12000eV_036.img │ │ │ ├── DRT240_12000eV_037.img │ │ │ ├── DRT240_12000eV_038.img │ │ │ ├── DRT240_12000eV_039.img │ │ │ ├── DRT240_12000eV_040.img │ │ │ ├── DRT240_12000eV_041.img │ │ │ ├── DRT240_12000eV_042.img │ │ │ ├── DRT240_12000eV_043.img │ │ │ ├── DRT240_12000eV_044.img │ │ │ ├── DRT240_12000eV_045.img │ │ │ ├── DRT240_12000eV_046.img │ │ │ └── DRT240_12000eV_047.img │ │ └── DRT322 │ │ │ ├── DRT322_10000eV_001.img │ │ │ ├── DRT322_10000eV_002.img │ │ │ ├── DRT322_10000eV_003.img │ │ │ ├── DRT322_10000eV_004.img │ │ │ ├── DRT322_10000eV_005.img │ │ │ ├── DRT322_10000eV_006.img │ │ │ ├── DRT322_10000eV_007.img │ │ │ ├── DRT322_10000eV_008.img │ │ │ ├── DRT322_10000eV_009.img │ │ │ ├── DRT322_10000eV_010.img │ │ │ ├── DRT322_10000eV_011.img │ │ │ ├── DRT322_10000eV_012.img │ │ │ ├── DRT322_10000eV_013.img │ │ │ ├── DRT322_10000eV_014.img │ │ │ ├── DRT322_10000eV_015.img │ │ │ ├── DRT322_10000eV_016.img │ │ │ ├── DRT322_10000eV_017.img │ │ │ ├── DRT322_10000eV_018.img │ │ │ ├── DRT322_10000eV_019.img │ │ │ ├── DRT322_10000eV_020.img │ │ │ ├── DRT322_10000eV_021.img │ │ │ ├── DRT322_10000eV_022.img │ │ │ ├── DRT322_10000eV_023.img │ │ │ ├── DRT322_10000eV_024.img │ │ │ ├── DRT322_10000eV_025.img │ │ │ ├── DRT322_10000eV_026.img │ │ │ ├── DRT322_10000eV_027.img │ │ │ ├── DRT322_10000eV_028.img │ │ │ ├── DRT322_10000eV_029.img │ │ │ ├── DRT322_10000eV_030.img │ │ │ ├── DRT322_11000eV_001.img │ │ │ ├── DRT322_11000eV_002.img │ │ │ ├── DRT322_11000eV_003.img │ │ │ ├── DRT322_11000eV_004.img │ │ │ ├── DRT322_11000eV_005.img │ │ │ ├── DRT322_11000eV_006.img │ │ │ ├── DRT322_11000eV_007.img │ │ │ ├── DRT322_11000eV_008.img │ │ │ ├── DRT322_11000eV_009.img │ │ │ ├── DRT322_11000eV_010.img │ │ │ ├── DRT322_11000eV_011.img │ │ │ ├── DRT322_11000eV_012.img │ │ │ ├── DRT322_11000eV_013.img │ │ │ ├── DRT322_11000eV_014.img │ │ │ ├── DRT322_11000eV_015.img │ │ │ ├── DRT322_11000eV_016.img │ │ │ ├── DRT322_11000eV_017.img │ │ │ ├── DRT322_11000eV_018.img │ │ │ ├── DRT322_11000eV_019.img │ │ │ ├── DRT322_11000eV_020.img │ │ │ ├── DRT322_11000eV_021.img │ │ │ ├── DRT322_11000eV_022.img │ │ │ ├── DRT322_11000eV_023.img │ │ │ ├── DRT322_11000eV_024.img │ │ │ ├── DRT322_11000eV_025.img │ │ │ ├── DRT322_11000eV_026.img │ │ │ ├── DRT322_11000eV_027.img │ │ │ ├── DRT322_11000eV_028.img │ │ │ ├── DRT322_11000eV_029.img │ │ │ └── DRT322_11000eV_030.img │ ├── raw │ │ └── q55 │ │ │ ├── DRT240 │ │ │ ├── e10000 │ │ │ │ ├── image_001.raw │ │ │ │ ├── image_002.raw │ │ │ │ ├── image_003.raw │ │ │ │ ├── image_004.raw │ │ │ │ ├── image_005.raw │ │ │ │ ├── image_006.raw │ │ │ │ ├── image_007.raw │ │ │ │ ├── image_008.raw │ │ │ │ ├── image_009.raw │ │ │ │ ├── image_010.raw │ │ │ │ ├── image_011.raw │ │ │ │ ├── image_012.raw │ │ │ │ ├── image_013.raw │ │ │ │ ├── image_014.raw │ │ │ │ ├── image_015.raw │ │ │ │ ├── image_016.raw │ │ │ │ ├── image_017.raw │ │ │ │ ├── image_018.raw │ │ │ │ ├── image_019.raw │ │ │ │ ├── image_020.raw │ │ │ │ ├── image_021.raw │ │ │ │ ├── image_022.raw │ │ │ │ ├── image_023.raw │ │ │ │ ├── image_024.raw │ │ │ │ ├── image_025.raw │ │ │ │ ├── image_026.raw │ │ │ │ ├── image_027.raw │ │ │ │ ├── image_028.raw │ │ │ │ ├── image_029.raw │ │ │ │ ├── image_030.raw │ │ │ │ ├── image_031.raw │ │ │ │ ├── image_032.raw │ │ │ │ ├── image_033.raw │ │ │ │ ├── image_034.raw │ │ │ │ ├── image_035.raw │ │ │ │ ├── image_036.raw │ │ │ │ ├── image_037.raw │ │ │ │ ├── image_038.raw │ │ │ │ ├── image_039.raw │ │ │ │ ├── image_040.raw │ │ │ │ ├── image_041.raw │ │ │ │ ├── image_042.raw │ │ │ │ ├── image_043.raw │ │ │ │ ├── image_044.raw │ │ │ │ ├── image_045.raw │ │ │ │ ├── image_046.raw │ │ │ │ └── image_047.raw │ │ │ ├── e11000 │ │ │ │ ├── image_001.raw │ │ │ │ ├── image_002.raw │ │ │ │ ├── image_003.raw │ │ │ │ ├── image_004.raw │ │ │ │ ├── image_005.raw │ │ │ │ ├── image_006.raw │ │ │ │ ├── image_007.raw │ │ │ │ ├── image_008.raw │ │ │ │ ├── image_009.raw │ │ │ │ ├── image_010.raw │ │ │ │ ├── image_011.raw │ │ │ │ ├── image_012.raw │ │ │ │ ├── image_013.raw │ │ │ │ ├── image_014.raw │ │ │ │ ├── image_015.raw │ │ │ │ ├── image_016.raw │ │ │ │ ├── image_017.raw │ │ │ │ ├── image_018.raw │ │ │ │ ├── image_019.raw │ │ │ │ ├── image_020.raw │ │ │ │ ├── image_021.raw │ │ │ │ ├── image_022.raw │ │ │ │ ├── image_023.raw │ │ │ │ ├── image_024.raw │ │ │ │ ├── image_025.raw │ │ │ │ ├── image_026.raw │ │ │ │ ├── image_027.raw │ │ │ │ ├── image_028.raw │ │ │ │ ├── image_029.raw │ │ │ │ ├── image_030.raw │ │ │ │ ├── image_031.raw │ │ │ │ ├── image_032.raw │ │ │ │ ├── image_033.raw │ │ │ │ ├── image_034.raw │ │ │ │ ├── image_035.raw │ │ │ │ ├── image_036.raw │ │ │ │ ├── image_037.raw │ │ │ │ ├── image_038.raw │ │ │ │ ├── image_039.raw │ │ │ │ ├── image_040.raw │ │ │ │ ├── image_041.raw │ │ │ │ ├── image_042.raw │ │ │ │ ├── image_043.raw │ │ │ │ ├── image_044.raw │ │ │ │ ├── image_045.raw │ │ │ │ ├── image_046.raw │ │ │ │ └── image_047.raw │ │ │ └── e12000 │ │ │ │ ├── image_001.raw │ │ │ │ ├── image_002.raw │ │ │ │ ├── image_003.raw │ │ │ │ ├── image_004.raw │ │ │ │ ├── image_005.raw │ │ │ │ ├── image_006.raw │ │ │ │ ├── image_007.raw │ │ │ │ ├── image_008.raw │ │ │ │ ├── image_009.raw │ │ │ │ ├── image_010.raw │ │ │ │ ├── image_011.raw │ │ │ │ ├── image_012.raw │ │ │ │ ├── image_013.raw │ │ │ │ ├── image_014.raw │ │ │ │ ├── image_015.raw │ │ │ │ ├── image_016.raw │ │ │ │ ├── image_017.raw │ │ │ │ ├── image_018.raw │ │ │ │ ├── image_019.raw │ │ │ │ ├── image_020.raw │ │ │ │ ├── image_021.raw │ │ │ │ ├── image_022.raw │ │ │ │ ├── image_023.raw │ │ │ │ ├── image_024.raw │ │ │ │ ├── image_025.raw │ │ │ │ ├── image_026.raw │ │ │ │ ├── image_027.raw │ │ │ │ ├── image_028.raw │ │ │ │ ├── image_029.raw │ │ │ │ ├── image_030.raw │ │ │ │ ├── image_031.raw │ │ │ │ ├── image_032.raw │ │ │ │ ├── image_033.raw │ │ │ │ ├── image_034.raw │ │ │ │ ├── image_035.raw │ │ │ │ ├── image_036.raw │ │ │ │ ├── image_037.raw │ │ │ │ ├── image_038.raw │ │ │ │ ├── image_039.raw │ │ │ │ ├── image_040.raw │ │ │ │ ├── image_041.raw │ │ │ │ ├── image_042.raw │ │ │ │ ├── image_043.raw │ │ │ │ ├── image_044.raw │ │ │ │ ├── image_045.raw │ │ │ │ ├── image_046.raw │ │ │ │ └── image_047.raw │ │ │ └── DRT322 │ │ │ ├── e10000 │ │ │ ├── image_001.raw │ │ │ ├── image_002.raw │ │ │ ├── image_003.raw │ │ │ ├── image_004.raw │ │ │ ├── image_005.raw │ │ │ ├── image_006.raw │ │ │ ├── image_007.raw │ │ │ ├── image_008.raw │ │ │ ├── image_009.raw │ │ │ ├── image_010.raw │ │ │ ├── image_011.raw │ │ │ ├── image_012.raw │ │ │ ├── image_013.raw │ │ │ ├── image_014.raw │ │ │ ├── image_015.raw │ │ │ ├── image_016.raw │ │ │ ├── image_017.raw │ │ │ ├── image_018.raw │ │ │ ├── image_019.raw │ │ │ ├── image_020.raw │ │ │ ├── image_021.raw │ │ │ ├── image_022.raw │ │ │ ├── image_023.raw │ │ │ ├── image_024.raw │ │ │ ├── image_025.raw │ │ │ ├── image_026.raw │ │ │ ├── image_027.raw │ │ │ ├── image_028.raw │ │ │ ├── image_029.raw │ │ │ └── image_030.raw │ │ │ └── e11000 │ │ │ ├── image_001.raw │ │ │ ├── image_002.raw │ │ │ ├── image_003.raw │ │ │ ├── image_004.raw │ │ │ ├── image_005.raw │ │ │ ├── image_006.raw │ │ │ ├── image_007.raw │ │ │ ├── image_008.raw │ │ │ ├── image_009.raw │ │ │ ├── image_010.raw │ │ │ ├── image_011.raw │ │ │ ├── image_012.raw │ │ │ ├── image_013.raw │ │ │ ├── image_014.raw │ │ │ ├── image_015.raw │ │ │ ├── image_016.raw │ │ │ ├── image_017.raw │ │ │ ├── image_018.raw │ │ │ ├── image_019.raw │ │ │ ├── image_020.raw │ │ │ ├── image_021.raw │ │ │ ├── image_022.raw │ │ │ ├── image_023.raw │ │ │ ├── image_024.raw │ │ │ ├── image_025.raw │ │ │ ├── image_026.raw │ │ │ ├── image_027.raw │ │ │ ├── image_028.raw │ │ │ ├── image_029.raw │ │ │ └── image_030.raw │ ├── rejected_samples.txt │ └── run_log.txt │ ├── run_outputs.txt │ ├── run_simulation.sh │ ├── simulate_data_collection.py │ └── yw │ ├── combined.gv │ ├── csv │ ├── extractfacts_annotation.csv │ ├── extractfacts_annotation_qualifies.csv │ ├── extractfacts_extract_source.csv │ ├── modelfacts_channel.csv │ ├── modelfacts_data.csv │ ├── modelfacts_function.csv │ ├── modelfacts_has_in_port.csv │ ├── modelfacts_has_out_port.csv │ ├── modelfacts_has_subprogram.csv │ ├── modelfacts_inflow_connects_to_channel.csv │ ├── modelfacts_outflow_connects_to_channel.csv │ ├── modelfacts_port.csv │ ├── modelfacts_port_alias.csv │ ├── modelfacts_port_connects_to_channel.csv │ ├── modelfacts_port_uri_template.csv │ ├── modelfacts_program.csv │ ├── modelfacts_uri_variable.csv │ ├── modelfacts_workflow.csv │ ├── reconfacts_data_resource.csv │ ├── reconfacts_resource.csv │ └── reconfacts_uri_variable_value.csv │ ├── dlv │ ├── extract_queries.dlv │ ├── extractfacts.dlv │ ├── model_queries.dlv │ ├── modelfacts.dlv │ ├── recon_queries.dlv │ ├── reconfacts.dlv │ ├── rules.dlv │ ├── run_queries.sh │ └── run_queries.txt │ ├── listing.txt │ ├── xsb │ ├── .gitignore │ ├── extract_facts.P │ ├── extract_queries.P │ ├── model_facts.P │ ├── model_queries.P │ ├── recon_facts.P │ ├── recon_queries.P │ ├── run_queries.sh │ ├── run_queries.txt │ └── xsb_rules.P │ ├── yw.properties │ ├── yw.properties.csv │ ├── yw.properties.dlv │ └── yw.properties.xsb ├── incoming ├── .DS_Store ├── AffyGeneExpressionAnalysisV12.R ├── DroughtTimeScale_Markup.m ├── DroughtTimeScale_Markup_v2.m ├── LTVTP_CAR.R ├── LTVTP_CAR.gv ├── LTVTP_CAR.pdf ├── comment_to_graph.py ├── example.py ├── foobar.py └── yw.properties ├── pom.xml ├── src ├── main │ ├── antlr4 │ │ ├── YW.g4 │ │ └── example.yw │ ├── java │ │ └── org │ │ │ └── yesworkflow │ │ │ ├── Language.java │ │ │ ├── LanguageModel.java │ │ │ ├── VersionInfo.java │ │ │ ├── YWKeywords.java │ │ │ ├── YWStage.java │ │ │ ├── YesWorkflowTestCase.java │ │ │ ├── annotations │ │ │ ├── AliasableAnnotation.java │ │ │ ├── Annotation.java │ │ │ ├── As.java │ │ │ ├── Begin.java │ │ │ ├── Call.java │ │ │ ├── Delimiter.java │ │ │ ├── Desc.java │ │ │ ├── End.java │ │ │ ├── FileUri.java │ │ │ ├── Flow.java │ │ │ ├── In.java │ │ │ ├── Log.java │ │ │ ├── Out.java │ │ │ ├── Param.java │ │ │ ├── Qualification.java │ │ │ ├── Return.java │ │ │ └── UriAnnotation.java │ │ │ ├── cli │ │ │ ├── ExitCode.java │ │ │ ├── YWCommand.java │ │ │ └── YesWorkflowCLI.java │ │ │ ├── config │ │ │ ├── Configurable.java │ │ │ ├── SettingLocation.java │ │ │ └── YWConfiguration.java │ │ │ ├── data │ │ │ ├── ConcreteUri.java │ │ │ ├── LogEntryTemplate.java │ │ │ ├── TemplateVariable.java │ │ │ ├── UriBase.java │ │ │ └── UriTemplate.java │ │ │ ├── db │ │ │ ├── Column.java │ │ │ ├── ColumnAlias.java │ │ │ ├── Table.java │ │ │ ├── TableAlias.java │ │ │ ├── View.java │ │ │ ├── YesWorkflowDB.java │ │ │ ├── YesWorkflowH2DB.java │ │ │ └── YesWorkflowSQLiteDB.java │ │ │ ├── exceptions │ │ │ ├── YWException.java │ │ │ ├── YWMarkupException.java │ │ │ └── YWToolUsageException.java │ │ │ ├── extract │ │ │ ├── CommentMatcher.java │ │ │ ├── DefaultExtractor.java │ │ │ ├── ExtractFacts.java │ │ │ ├── Extractor.java │ │ │ ├── HashmapMatlabWrapper.java │ │ │ ├── KeywordMatcher.java │ │ │ └── SkeletonBuilder.java │ │ │ ├── graph │ │ │ ├── CommentVisibility.java │ │ │ ├── DataLabelMode.java │ │ │ ├── DotBuilder.java │ │ │ ├── DotGrapher.java │ │ │ ├── EdgeLabelMode.java │ │ │ ├── ElementStyleView.java │ │ │ ├── GraphFormat.java │ │ │ ├── GraphView.java │ │ │ ├── Grapher.java │ │ │ ├── LayoutClusterView.java │ │ │ ├── LayoutDirection.java │ │ │ ├── ParamVisibility.java │ │ │ ├── PortLayout.java │ │ │ ├── ProgramLabelMode.java │ │ │ ├── TitlePosition.java │ │ │ └── WorkflowBoxMode.java │ │ │ ├── model │ │ │ ├── Channel.java │ │ │ ├── Data.java │ │ │ ├── DefaultModeler.java │ │ │ ├── Function.java │ │ │ ├── Model.java │ │ │ ├── ModelFacts.java │ │ │ ├── Modeler.java │ │ │ ├── Port.java │ │ │ ├── Program.java │ │ │ ├── Workflow.java │ │ │ └── WorkflowBuilder.java │ │ │ ├── query │ │ │ ├── CSVExportBuilder.java │ │ │ ├── DataExportBuilder.java │ │ │ ├── FactsExportBuilder.java │ │ │ ├── QueryEngine.java │ │ │ └── QueryEngineModel.java │ │ │ ├── recon │ │ │ ├── DefaultReconstructor.java │ │ │ ├── FileResourceFinder.java │ │ │ ├── ReconFacts.java │ │ │ ├── Reconstructor.java │ │ │ ├── Resource.java │ │ │ ├── ResourceFinder.java │ │ │ └── Run.java │ │ │ └── util │ │ │ └── FileIO.java │ ├── python │ │ ├── README.txt │ │ ├── csv2gv │ │ ├── dots.py │ │ ├── example.gv │ │ ├── example.pdf │ │ └── script2csv │ └── resources │ │ ├── MyScript.png │ │ ├── MyScript.py │ │ ├── MyScript_combined.png │ │ ├── example.pdf │ │ ├── example.py │ │ ├── example_combined.gv │ │ ├── example_combined.png │ │ ├── example_comments.txt │ │ ├── example_data.gv │ │ ├── example_data.png │ │ ├── example_process.gv │ │ ├── example_process.png │ │ ├── example_skeleton.txt │ │ ├── maven.properties │ │ └── org │ │ └── yesworkflow │ │ └── db │ │ ├── h2 │ │ ├── createtables.h2 │ │ ├── generate.sh │ │ └── pom.xml │ │ └── sqlite │ │ ├── createtables.sqlite │ │ ├── generate.sh │ │ └── pom.xml └── test │ ├── .DS_Store │ ├── java │ ├── .DS_Store │ └── org │ │ ├── .DS_Store │ │ └── yesworkflow │ │ ├── .DS_Store │ │ ├── annotations │ │ ├── TestBegin.java │ │ ├── TestDesc.java │ │ ├── TestEnd.java │ │ ├── TestIn.java │ │ ├── TestInWithUri.java │ │ ├── TestOut.java │ │ ├── TestOutWithUri.java │ │ └── TestParam.java │ │ ├── cli │ │ └── TestYesWorkflowCLI.java │ │ ├── config │ │ └── TestYWConfiguration.java │ │ ├── data │ │ ├── TestLogEntryTemplate.java │ │ ├── TestUri.java │ │ ├── TestUriBase.java │ │ └── TestUriTemplate.java │ │ ├── db │ │ ├── TestYesWorkflowDB.java │ │ └── TestYesWorkflowDBViews.java │ │ ├── extract │ │ ├── TestCommentMatcher_Bash.java │ │ ├── TestCommentMatcher_Java.java │ │ ├── TestCommentMatcher_Matlab.java │ │ ├── TestCommentMatcher_SAS.java │ │ ├── TestDefaultExtractor.java │ │ ├── TestExtractFacts.java │ │ └── TestSkeletonBuilder.java │ │ ├── graph │ │ ├── DotGrapherTestCase.java │ │ ├── TestDotGrapher_CombinedView.java │ │ ├── TestDotGrapher_DataView.java │ │ ├── TestDotGrapher_ProcessView.java │ │ └── TestDotGrapher_SimulateDataCollection.java │ │ ├── model │ │ ├── TestDefaultModeler.java │ │ ├── TestDefaultModer_ExtractTopPorts.java │ │ └── TestModeler_Functions.java │ │ └── recon │ │ └── TestDefaultReconstructor.java │ └── resources │ ├── branchExample.py │ ├── org │ └── yesworkflow │ │ ├── config │ │ ├── config_bad.yaml │ │ ├── config_increasing_nesting.properties │ │ ├── config_increasing_nesting.yaml │ │ ├── config_nested.properties │ │ ├── config_nested.yaml │ │ └── config_three_types.yaml │ │ ├── graph │ │ ├── TestDotGrapher_CombinedView │ │ │ ├── examplePyScript.gv │ │ │ ├── examplePyScript.in │ │ │ ├── twoChannels_OneProgram_OneInOneOut.gv │ │ │ ├── twoChannels_OneProgram_OneInOneOut.in │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut.gv │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut.in │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut_HideParams.gv │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut_ReduceParams.gv │ │ │ ├── twoChannels_OneProgram_TwoInOneOut.gv │ │ │ ├── twoChannels_OneProgram_TwoInOneOut.in │ │ │ ├── twoProgramsOneChannel_InOut.gv │ │ │ ├── twoProgramsOneChannel_InOut.in │ │ │ ├── twoProgramsOneChannel_ParamOut.gv │ │ │ └── twoProgramsOneChannel_ParamOut.in │ │ ├── TestDotGrapher_DataView │ │ │ ├── twoChannels_OneProgram_OneInOneOut.gv │ │ │ ├── twoChannels_OneProgram_OneInOneOut.in │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut.in │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut_HideParams.gv │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut_ReduceParams.gv │ │ │ ├── twoChannels_OneProgram_OneInOneParamOneOut_ShowParams.gv │ │ │ ├── twoChannels_OneProgram_OneParamOneOut.in │ │ │ ├── twoChannels_OneProgram_OneParamOneOut_HideParams.gv │ │ │ ├── twoChannels_OneProgram_OneParamOneOut_ReduceParams.gv │ │ │ ├── twoChannels_OneProgram_OneParamOneOut_ShowParams.gv │ │ │ ├── twoChannels_OneProgram_TwoInOneOut.gv │ │ │ ├── twoChannels_OneProgram_TwoInOneOut.in │ │ │ ├── twoProgramsOneChannel_OneInOneOut.gv │ │ │ ├── twoProgramsOneChannel_OneInOneOut.in │ │ │ ├── twoProgramsOneChannel_OneParamOneOut.in │ │ │ ├── twoProgramsOneChannel_OneParamOneOut_HideParams.gv │ │ │ └── twoProgramsOneChannel_OneParamOneOut_ShowParams.gv │ │ └── TestDotGrapher_ProcessView │ │ │ ├── doublyNestedSubworkflow.gv │ │ │ ├── doublyNestedSubworkflow.in │ │ │ ├── doublyNestedSubworkflow_sub.gv │ │ │ ├── doublyNestedSubworkflow_subSub.gv │ │ │ ├── examplePyScript.gv │ │ │ ├── examplePyScript.in │ │ │ ├── nestedSubworkflow.gv │ │ │ ├── nestedSubworkflow.in │ │ │ ├── nestedSubworkflow_sub.gv │ │ │ ├── oneProgram_ThreeChannels_TwoInOneOut.gv │ │ │ ├── oneProgram_ThreeChannels_TwoInOneOut.in │ │ │ ├── oneProgram_TwoChannels_OneInOneOut.gv │ │ │ ├── oneProgram_TwoChannels_OneInOneOut.in │ │ │ ├── oneProgram_TwoChannels_OneInOneOut_ExtraOut.gv │ │ │ ├── oneProgram_TwoChannels_OneInOneOut_ExtraOut.in │ │ │ ├── oneProgram_TwoChannels_OneInOneOut_HideParams.gv │ │ │ ├── oneProgram_TwoChannels_OneInOneOut_VerticalLayout.gv │ │ │ ├── oneProgram_TwoChannels_OneParamOneInOneOut.gv │ │ │ ├── oneProgram_TwoChannels_OneParamOneInOneOut.in │ │ │ ├── oneProgram_TwoChannels_OneParamOneInOneOut_HideParams.gv │ │ │ ├── oneProgram_TwoChannels_OneParamOneOut.gv │ │ │ ├── oneProgram_TwoChannels_OneParamOneOut.in │ │ │ ├── oneProgram_TwoChannels_OneParamOneOut_HideParams.gv │ │ │ ├── oneProgram_TwoInOneOut_ExtraIn.gv │ │ │ ├── oneProgram_TwoInOneOut_ExtraIn.in │ │ │ ├── threePrograms_TwoChannels.gv │ │ │ ├── threePrograms_TwoChannels.in │ │ │ ├── twoProgramsOneChannel_In.gv │ │ │ ├── twoProgramsOneChannel_In.in │ │ │ └── twoProgramsOneChannel_Param.gv │ │ └── testYesWorkflowCLI │ │ ├── extensionlessSource │ │ ├── git.properties │ │ ├── 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